=head1 NAME

cdparser module - part of the Wise2 package

=head1 SYNOPSIS

This module contains the following objects

=over

=item cDNAParser


=back

=head1 DESCRIPTION

=head2 Object cDNAParser

=over

=item trans[PCD_PARSER_TRANS_LEN]

 Type [Probability] Scalar No documentation



=back

This object holds the (very few) extra
transition information needed for the
estwise algorithm. It is sort of like
the 'gene model' part of sequencing
error (but very very simple)




=head2 Member functions of cDNAParser

=over

=item hard_link_cDNAParser

&Wise2::cDNAParser::hard_link_cDNAParser(obj)

  Bumps up the reference count of the object
  Meaning that multiple pointers can 'own' it



  Argument obj          [UNKN ] Object to be hard linked [cDNAParser *]
  Return [UNKN ] Undocumented return value [cDNAParser *]


=item alloc

&Wise2::cDNAParser::alloc(void)

  Allocates structure: assigns defaults if given 



  Return [UNKN ] Undocumented return value [cDNAParser *]


=back

=over

=item flat_cDNAParser

&Wise2::flat_cDNAParser(p)

  Makes a flat (ie, indels of 1 or 2 == p)
  cDNA parser. This means that insertions
  and deletions of both 1 or 2 bases are
  all parameterised at the same probability




  Argument p            [READ ] probability of an indel [Probability]
  Return [UNKN ] Undocumented return value [cDNAParser *]


=back