<commit_before>package Bio::EnsEMBL::GlyphSet::tsv_variations;

use strict;

use Sanger::Graphics::Bump;
use Bio::EnsEMBL::Variation::Utils::Sequence qw(ambiguity_code);

use base qw(Bio::EnsEMBL::GlyphSet);

sub _init {
  my ($self) = @_;
  my $check = $self->check();
  return unless defined $check;
  return unless $self->strand() == -1;

  my $Config        = $self->{'config'};  
  my $transcript = $Config->{'transcript'}->{'transcript'}; 
  my $consequences_ref = $Config->{'transcript'}->{'consequences'}; 
  my $alleles      = $Config->{'transcript'}->{'allele_info'};
  return unless $alleles && $consequences_ref;

  # Drawing params
  my( $fontname, $fontsize ) = $self->get_font_details( 'innertext' );
  my $pix_per_bp    = $Config->transform->{'scalex'};
  my @res = $self->get_text_width( 0, 'M', '', 'font'=>$fontname, 'ptsize' => $fontsize );
  my( $font_w_bp, $font_h_bp) = ($res[2]/$pix_per_bp,$res[3]);
  my $height = $res[3] + 4;   

  # Bumping params
  my $pix_per_bp    = $Config->transform->{'scalex'};
  my $bitmap_length = int($Config->container_width() * $pix_per_bp);
  my $voffset = 0;
  my @bitmap;

  # Data stuff
  my $colour_map = $self->my_config('colours');
  my $EXTENT        = $Config->get_parameter( 'context')|| 1e6;
     $EXTENT        = 1e6 if $EXTENT eq 'FULL';
  warn "######## ERROR arrays should be same length" unless length @$alleles == length @$consequences_ref;

<commit_msg>use type instead of check<commit_after>package Bio::EnsEMBL::GlyphSet::tsv_variations;

use strict;

use Sanger::Graphics::Bump;
use Bio::EnsEMBL::Variation::Utils::Sequence qw(ambiguity_code);

use base qw(Bio::EnsEMBL::GlyphSet);

sub _init {
  my ($self) = @_;
  my $check = $self->type;
  return unless defined $check;
  return unless $self->strand() == -1;

  my $Config        = $self->{'config'};  
  my $transcript = $Config->{'transcript'}->{'transcript'}; 
  my $consequences_ref = $Config->{'transcript'}->{'consequences'}; 
  my $alleles      = $Config->{'transcript'}->{'allele_info'};
  return unless $alleles && $consequences_ref;

  # Drawing params
  my( $fontname, $fontsize ) = $self->get_font_details( 'innertext' );
  my $pix_per_bp    = $Config->transform->{'scalex'};
  my @res = $self->get_text_width( 0, 'M', '', 'font'=>$fontname, 'ptsize' => $fontsize );
  my( $font_w_bp, $font_h_bp) = ($res[2]/$pix_per_bp,$res[3]);
  my $height = $res[3] + 4;   

  # Bumping params
  my $pix_per_bp    = $Config->transform->{'scalex'};
  my $bitmap_length = int($Config->container_width() * $pix_per_bp);
  my $voffset = 0;
  my @bitmap;

  # Data stuff
  my $colour_map = $self->my_config('colours');
  my $EXTENT        = $Config->get_parameter( 'context')|| 1e6;
     $EXTENT        = 1e6 if $EXTENT eq 'FULL';
  warn "######## ERROR arrays should be same length" unless length @$alleles == length @$consequences_ref;


{'fraction_non_alphanumeric': 0.19280475026196298, 'fraction_numerical': 0.007684247293049249, 'mean_word_length': 4.353271028037383, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 43, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4930921', 'n_tokens_mistral': 1097, 'n_tokens_neox': 1045, 'n_words': 226}