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  $class->runtime_prop->{command}->{split_or_splice} ;
}


=head2 split_or_splice_for_pe

 Alien::SeqAlignment::last->split_or_splice_for_pe

This commnd provides access to last-split, which finds "split alignments" 
(typically for DNA) or "spliced alignments" (typically for RNA). It 
specifically targets paired-end reads. 
last-split-pe is a method that can split-align a short DNA read to a 
reference genome. It achieves high accuracy by combining probabilistic 
alignments with information from paired-end reads.

=cut

sub split_or_splice_pe {
    my ($class) = @_;
  $class->runtime_prop->{command}->{split_or_splice_pe} ;
}

=head2 pe_probs

 Alien::SeqAlignment::last->pe_probs

This commnd provides access to last-pair-probs, which reads candidate 
alignments of paired DNA reads to a genome, and:

* estimates the distribution of distances between paired reads,
* estimates the probability that each alignment represents the
genomic source of the read.
These probabilities corresponds to a split alignment of the pair end
read. 
=cut

sub pe_probs {
    my ($class) = @_;
  $class->runtime_prop->{command}->{pe_probs} ;
}

=head1 SEE ALSO

=over 4

=item * L<LAST|https://gitlab.com/mcfrith/last/-/tree/main>

LAST: find & align related regions of sequences
LAST is designed for moderately large data (e.g. genomes, DNA reads,
proteomes).  It's especially good at:

* Finding rearrangements and recombinations: the primary author claims 
that last-split does that more rigorously than anything else.
* Finding DNA-versus-protein related regions, especially protein
fossils.
* Unusual data, e.g. AT-rich DNA, because we can fit parameters to
the data and calculate significance.
* Sensitive DNA-DNA search, due to fitting, sensitive seeding, and
calculating significance.

It can also: indicate the confidence/uncertainty of each column in an
alignment, and use sequence quality data in a rigorous fashion.

=item * L<last-split-pe|https://bitbucket.org/splitpairedend/last-split-pe/wiki/Home>

last-split-pe is a method that can split-align a short DNA read to a 
reference genome. It achieves high accuracy by combining probabilistic 
alignments with information from paired-end reads.

=item * L<Alien>

Documentation on the Alien concept itself.

=item * L<Alien::Base|https://metacpan.org/pod/Alien::Base>

The base class for this Alien. The methods in that class allow you to use
the static and the dynamic edlib library in your code. 

=item * L<Alien::Build::Manual::AlienUser|https://metacpan.org/dist/Alien-Build/view/lib/Alien/Build/Manual/AlienUser.pod>

Detailed manual for users of Alien classes.

=item * L<Bio::SeqAlignment|https://metacpan.org/pod/Bio::SeqAlignment>

A collection of tools and libraries for aligning biological sequences 
from within Perl. 

=back

=head1 AUTHOR

Christos Argyropoulos <chrisarg@gmail.com>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2024 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.

=cut

1;