File Coverage

blib/lib/Bio/Gonzales/Seq/IO/fastq.pm

Criterion	Covered	Total	%
statement	29	41	70.7
branch	5	10	50.0
condition			n/a
subroutine	6	7	85.7
pod	1	1	100.0
total	41	59	69.4

package Bio::Gonzales::Seq::IO::fastq;

use Mouse;

use warnings;
use strict;

use 5.010;

our $VERSION = '0.083'; # VERSION

our %VARIANT = (
  sanger => {
    'ascii_offset' => 33,
    'q_start'      => 0,
    'q_end'        => 93
  },
  solexa => {
    'ascii_offset' => 64,
    'q_start'      => -5,
    'q_end'        => 62
  },
  illumina => {
    'ascii_offset' => 64,
    'q_start'      => 0,
    'q_end'        => 62
  },
);

has cache         => ( is => 'rw' );
has variant       => ( is => 'rw', default => 'sanger' );
has _ascii_offset => ( is => 'rw' );

sub BUILD {
  my ($self) = @_;

  if    ( $self->variant eq 'solexa' )   { $self->_cache_solexa }
  elsif ( $self->variant eq 'illumina' ) { $self->_cache_non_solexa }
  elsif ( $self->variant eq 'sanger' )   { $self->_cache_non_solexa }
}

sub _cache_solexa {
  my ($self) = @_;

  my ( @c2q, @q2c, @sol2phred, %phred_fp2chr, @phred_int2chr );

  my $ascii_offset = $VARIANT{'solexa'}{'ascii_offset'};
  for ( my $i = 0; $i < $VARIANT{'solexa'}{'q_end'} - $VARIANT{'solexa'}{'q_start'} + 1; $i++ ) {
    my $q = $i + $VARIANT{'solexa'}{'q_start'};
    my $c = $q + $ascii_offset;
    $c2q[$c] = $q;
    $q2c[$i] = chr($c);

    # solexa <=> solexa mapping speedup (retain floating pt precision)
    my $s2p = 10 * log( 1 + 10**( $q / 10.0 ) ) / log(10);
    $sol2phred[$i] = $s2p;

    $phred_fp2chr{$s2p} = chr($c);

    next if $q < 0;    # skip loop; PHRED scores greater than 0
    my $p2s = sprintf( "%.0f", ( $q <= 1 ) ? -5 : 10 * log( -1 + 10**( $q / 10.0 ) ) / log(10) );
    # sanger/illumina PHRED <=> Solexa char mapping speedup
    $phred_int2chr[$i] = chr( $p2s + $ascii_offset );
  }
  $self->cache(
    {
      c2q           => \@c2q,
      q2c           => \@q2c,
      sol2phred     => \@sol2phred,
      phred_fp2chr  => \%phred_fp2chr,
      phred_int2chr => \@phred_int2chr,
      q_start       => $VARIANT{'solexa'}{'q_start'},
      q_end         => $VARIANT{'solexa'}{'q_end'},
      ascii_offset  => $ascii_offset,
    }
  );
}

sub _cache_non_solexa {
  my ($self) = @_;
  my $enc = $self->variant;
  my ( @c2q, @q2c );

  my $ascii_offset = $VARIANT{$enc}{'ascii_offset'};
  for ( my $i = 0; $i < $VARIANT{$enc}{'q_end'} - $VARIANT{$enc}{'q_start'} + 1; $i++ ) {
    my $q = $i + $VARIANT{$enc}{'q_start'};
    my $c = $q + $ascii_offset;
    $c2q[$c] = $q;
    $q2c[$i] = chr($c);

  }
  $self->cache(
    {
      c2q          => \@c2q,
      q2c          => \@q2c,
      q_start      => $VARIANT{$enc}{'q_start'},
      q_end        => $VARIANT{$enc}{'q_end'},
      ascii_offset => $ascii_offset

    }
  );
}

__PACKAGE__->meta->make_immutable;

1;