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lib/CracTools/SAMReader/SAMline.pm  view on Meta::CPAN

  return $self;
}


sub isFlagged {
  my $self = shift;
  my $flag = shift;
  return $self->flag & $flag;
}


sub getStrand {
  my $self = shift;
  if($self->isFlagged($flags{REVERSE_COMPLEMENTED})) {
    return -1;
  } else {
    return 1;
  }
}


sub getOriginalSeq {
  my $self = shift;
  if($self->isFlagged($flags{REVERSE_COMPLEMENTED})) {
    return CracTools::Utils::reverseComplement($self->seq);
  } else {
    return $self->seq;
  }
}


sub getLocAsCracFormat {
  my $self = shift;
  return $self->rname."|".$self->getStrand.",".$self->pos;
}


sub getPatch {
  my $self = shift;
  my $line_number = shift;
  croak("Cannot generate patch without the line number in argument") unless defined $line_number;
  if($self->updatedLine ne $self->line) {
    my $line1 = $self->line;
    my $line2 = $self->updatedLine;
    chomp($line1);
    chomp($line2);
    return "@@ -$line_number,1 +$line_number,1 @@\n-$line1\n+$line2";
  } else {
    return 0;
  }
}



sub line {
  my $self = shift;
  return $self->{line};
}


sub updatedLine {
  my $self = shift;
  my $updated_line = shift;
  if(defined $updated_line) {
    $self->{updated_line} = $updated_line;
    return 1;
  } elsif (!defined $self->{updated_line}) {
    return $self->line;
  } else {
    return $self->{updated_line};
  }
}


sub qname {
  my $self = shift;
  my $new_qname = shift;
  if(defined $new_qname) {
    $self->{qname} = $new_qname;
  }
  return $self->{qname};
}


sub flag {
  my $self = shift;
  my $new_flag = shift;
  if(defined $new_flag) {
    $self->{flag} = $new_flag;
  }
  return $self->{flag};
}


sub rname {
  my $self = shift;
  my $new_rname = shift;
  if(defined $new_rname) {
    $self->{rname} = $new_rname;
  }
  return $self->{rname};
}


sub chr {
  my $self = shift;
  $self->rname(@_);
}


sub pos {
  my $self = shift;
  my $new_pos = shift;
  if(defined $new_pos) {
    $self->{pos} = $new_pos;
  }
  return $self->{pos};
}


sub mapq {

lib/CracTools/SAMReader/SAMline.pm  view on Meta::CPAN

                      score => $score,
                    );
        } elsif($event_type eq 'undetermined') {
          %event_hash = ( message => $event_infos,
                    );
        } elsif($event_type eq 'bioundetermined') {
          my ($pos,$message) = $event_infos =~ /([^:]+):(.*)/; 
          %event_hash = ( pos => $pos,
                      message => $message,
                    );
        }
        if (keys %event_hash > 1) {
          $event_hash{event_id} = $event_id;
          $event_hash{break_id} = $event_break_id;
          $event_hash{event_type} = $event_type;
          $self->addEvent(\%event_hash);
        }
      }
    }
    ## If we have only load a specific event type
    #if(defined $event_type_to_load) {
    #  $self->{$event_type_to_load}{loaded} = 1;
    ## Else we have load every events.
    #} else {
    #  $self->{events}{loaded} = 1;
    #}
  }
}


sub addEvent {
  my $self = shift;
  my $event = shift;
  my $event_type = $event->{event_type};
  if(defined $self->{events}{$event_type}) {
    push(@{$self->{events}{$event_type}},$event);
  } else {
    $self->{events}{$event_type} = [$event];
  }
}


sub removeEvent {
  my $self = shift;
  my $delete_event = shift;
  my $type = $delete_event->{event_type};
  if(defined $type && defined $self->{events}{$type}) {
    my $i = 0;
    foreach my $event (@{$self->{events}{$type}}) {
      if($event eq $delete_event) {
        splice @{$self->{events}{$type}}, $i, 1;
        return 1;
      }
      $i++;
    }
  }
  return 0;
}


sub updateEvent {
  my $self = shift;
  my $event = shift;
  my $new_event_type = shift;
  my %new_event = @_;

  # Update new event with old break id and event id
  $new_event{event_type} = $new_event_type;
  $new_event{event_id} = $event->{event_id};
  $new_event{break_id} = $event->{break_id};

  if($self->removeEvent($event)) {
    # Catch warnings on string concatenation that correspond to missing
    # field in the hash for the event to update
    local $SIG{'__WARN__'} = sub {croak("Invalid event hash for event type '$new_event_type'");};
    my $base_XE = 'XE:Z:'.$new_event{event_id}.':'.$new_event{break_id};
    my $new_XE = $base_XE . ':';
    if($new_event_type eq 'Junction') {
        my $loc = compressCracLoc($new_event{loc}{chr},$new_event{loc}{pos},$new_event{loc}{strand});
        $new_XE .= $new_event_type.':'.
                   $new_event{type}.':'.
                   $new_event{pos}.':'.
                   $loc.':'.
                   $new_event{gap};
    } elsif($new_event_type eq 'Ins' || $new_event_type eq 'Del') {
        my $loc = compressCracLoc($new_event{loc}{chr},$new_event{loc}{pos},$new_event{loc}{strand});
        $new_XE .= $new_event_type.':'.
                   $new_event{score}.':'.
                   $new_event{pos}.':'.
                   $loc.':'.
                   $new_event{nb};
    } elsif($new_event_type eq 'SNP') {
        my $loc = compressCracLoc($new_event{loc}{chr},$new_event{loc}{pos},$new_event{loc}{strand});
        $new_XE .= $new_event_type.':'.
                   $new_event{score}.':'.
                   $new_event{pos}.':'.
                   $loc.':'.
                   $new_event{expected}.':'.
                   $new_event{actual};
    } elsif($new_event_type eq 'Error') {
        my $loc = compressCracLoc($new_event{loc}{chr},$new_event{loc}{pos},$new_event{loc}{strand});
        $new_XE .= $new_event_type.':'.
                   $new_event{type}.':'.
                   $new_event{pos}.':'.
                   $new_event{score}.':'.
                   $new_event{other1}.':'.
                   $new_event{other2};
    } elsif($new_event_type eq 'chimera') {
        my $loc1 = compressCracLoc($new_event{loc1}{chr},$new_event{loc1}{pos},$new_event{loc1}{strand});
        my $loc2 = compressCracLoc($new_event{loc2}{chr},$new_event{loc2}{pos},$new_event{loc2}{strand});
        $new_XE .= $new_event_type.':'.
                   $new_event{pos}.':'.
                   $loc1.':'.
                   $loc2;
    } elsif($new_event_type eq 'Undetermined') {
        $new_XE .= $new_event_type.':'.
                   $new_event{message};
    } elsif($new_event_type eq 'BioUndetermined') {
        $new_XE .= $new_event_type.':'.
                   $new_event{pos}.':'.
                   $new_event{message};