=pod

=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=head1 NAME

Bio::EnsEMBL::IO::Parser::VEP_output - A line-based parser for Ensembl's 
output format for the Variant Effect Predictor

=cut

package Bio::EnsEMBL::IO::Parser::VEP_output;

use strict;
use warnings;

use parent qw/Bio::EnsEMBL::IO::ColumnBasedParser/;
=head2 open

    Constructor
    Argument [1] : Filepath
    Argument [2+]: Hash of parameters for configuration, e.g. buffer sizes or 
                   specific functions for handling headers or data
    Returntype   : Bio::EnsEMBL::IO::TrackBasedParser

=cut

sub open {
    my ($caller, $filename, @other_args) = @_;
    my $class = ref($caller) || $caller;
    my $self;

    $self = $class->SUPER::open($filename, '\t|\s+', @other_args);

    if ($filename) {
      # pre-load peek buffer
      $self->next_block();
    }

    return $self;
}

sub is_metadata {
    my $self = shift;
    return $self->{'current_block'} =~ /^#/;
}

sub read_metadata {
### No useful metadata, just column names
  return;
}

=head2 set_fields

    Description: Setter for list of fields used in this format - uses the
                  "public" (i.e. non-raw) names of getter methods
    Returntype : Void

=cut

sub set_fields {
  my $self = shift;
  $self->{'fields'} = [qw(uploaded_variation location allele gene feature feature_type consequence cdna_position cds_position protein_position amino_acids codons existing_variant extra)]; 
}


=head2 get_raw_uploaded_variation

    Description: Getter for uploaded_variation field
    Returntype : String 

=cut

sub get_raw_uploaded_variation {
  my $self = shift;
  return $self->{'record'}[0];
}

=head2 get_uploaded_variation

    Description: Getter - wrapper around raw method 
    Returntype : String 

=cut

sub get_uploaded_variation {
  my $self = shift;
  return $self->get_raw_uploaded_variation();
}


=head2 get_raw_location

    Description: Getter for  field
    Returntype : String 

=cut

sub get_raw_location {
  my $self = shift;
  return $self->{'record'}[1];
}

=head2 get_seqname

    Description: Getter - munges data from raw_location method 
    Returntype : String 

=cut

sub get_seqname {
  my $self = shift;
  my ($seqname) = split(':', $self->get_raw_location());
  return $seqname;
}

=head2 get_start

    Description: Getter - munges data from raw_location method 
    Returntype : Integer 

=cut

sub get_start {
  my $self = shift;
  my ($seqname, $coords) = split(':', $self->get_raw_location());
  my ($start, $end) = split('-', $coords);
  return $start;
}

=head2 get_end

    Description: Getter - munges data from raw_location method
    Returntype : Integer 

=cut

sub get_end {
  my $self = shift;
  my ($seqname, $coords) = split(':', $self->get_raw_location());
  my ($start, $end) = split('-', $coords);
  return $end || $start;
}

=head2 get_raw_allele

    Description: Getter for allele field
    Returntype : String 

=cut

sub get_raw_allele {
  my $self = shift;
  return $self->{'record'}[2];
}

=head2 get_allele

    Description: Getter - wrapper around get_raw_allele
    Returntype : String

=cut

sub get_allele {
  my $self = shift;
  return $self->get_raw_allele();
}

=head2 get_raw_gene

    Description: Getter for  field
    Returntype : String (stable ID) 

=cut

sub get_raw_gene {
  my $self = shift;
  return $self->{'record'}[3];
}

=head2 get_gene

    Description: Getter - wrapper around raw method 
    Returntype : String 

=cut

sub get_gene {
  my $self = shift;
  return $self->get_raw_gene();
}

=head2 get_raw_feature

    Description: Getter for feature field
    Returntype : String (stable id)

=cut

sub get_raw_feature {
  my $self = shift;
  return $self->{'record'}[4];
}

=head2 get_feature

    Description: Getter - wrapper around raw method 
    Returntype : String 

=cut

sub get_feature {
  my $self = shift;
  return $self->get_raw_feature();
}

=head2 get_raw_feature_type

    Description: Getter for feature_type field
    Returntype : String 

=cut

sub get_raw_feature_type {
  my $self = shift;
  return $self->{'record'}[5];
}

=head2 get_feature_type

    Description: Getter - wrapper around raw method 
    Returntype : String 

=cut

sub get_feature_type {
  my $self = shift;
  return $self->get_raw_feature_type();
}

=head2 get_raw_consequence

    Description: Getter for consequence field
    Returntype : String 

=cut

sub get_raw_consequence {
  my $self = shift;
  return $self->{'record'}[6];
}

=head2 get_consequence

    Description: Getter - wrapper around raw method 
    Returntype : String 

=cut

sub get_consequence {
  my $self = shift;
  return $self->get_raw_consequence();
}

=head2 get_raw_cdna_position

    Description: Getter for cdna_position field
    Returntype : Integer

=cut

sub get_raw_cdna_position {
  my $self = shift;
  return $self->{'record'}[7];
}

=head2 get_cdna_position

    Description: Getter - wrapper around raw method 
    Returntype : Integer

=cut

sub get_cdna_position {
  my $self = shift;
  return $self->get_raw_cdna_position();
}

=head2 get_raw_cds_position

    Description: Getter for cds_position field
    Returntype : Integer

=cut

sub get_raw_cds_position {
  my $self = shift;
  return $self->{'record'}[8];
}

=head2 get_cds_position

    Description: Getter - wrapper around raw method 
    Returntype : Integer 

=cut

sub get_cds_position {
  my $self = shift;
  return $self->get_raw_cds_position();
}

=head2 get_raw_protein_position

    Description: Getter for protein_position field
    Returntype : Integer

=cut

sub get_raw_protein_position {
  my $self = shift;
  return $self->{'record'}[9];
}

=head2 get_protein_position

    Description: Getter - wrapper around raw method 
    Returntype : Integer

=cut

sub get_protein_position {
  my $self = shift;
  return $self->get_raw_protein_position();
}

=head2 get_raw_amino_acids

    Description: Getter for amino_acids field
    Returntype : String 

=cut

sub get_raw_amino_acids {
  my $self = shift;
  return $self->{'record'}[10];
}

=head2 get_amino_acids

    Description: Getter - wrapper around raw method 
    Returntype : String 

=cut

sub get_amino_acids {
  my $self = shift;
  return $self->get_raw_amino_acids();
}

=head2 get_raw_codons

    Description: Getter for codons field
    Returntype : String 

=cut

sub get_raw_codons {
  my $self = shift;
  return $self->{'record'}[11];
}

=head2 get_codons

    Description: Getter - wrapper around raw method 
    Returntype : String 

=cut

sub get_codons {
  my $self = shift;
  return $self->get_raw_codons();
}

=head2 get_raw_existing_variation

    Description: Getter for colocated field
    Returntype : String 

=cut

sub get_raw_existing_variation {
  my $self = shift;
  return $self->{'record'}[12];
}

=head2 get_existing_variation

    Description: Getter - wrapper around raw method 
    Returntype : String 

=cut

sub get_existing_variation {
  my $self = shift;
  return $self->get_raw_existing_variation();
}

=head2 get_raw_extra

    Description: Getter for extra field
    Returntype : String 

=cut

sub get_raw_extra {
  my $self = shift;
  return $self->{'record'}[13];
}

=head2 get_extra

    Description: Getter - wrapper around raw method 
    Returntype : Hashref 

=cut

sub get_extra {
  my $self = shift;
  my $raw_extra = $self->get_raw_extra();
  my $extra = {};
  my @A = split(';', $raw_extra);
  foreach (@A) {
    my ($k, $v) = split('=', $_);
    $extra->{$k} = $v;
  }
  return $extra;
}


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