GenOO::Data::File::SAM::Record - Object representing a record of a sam file
# Object representing a record of a sam file # To initialize my $sam_record = GenOO::Data::File::SAM::Record->new( fields => [qname,flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual, tags] );
This object represents a record of a sam file and offers methods for accessing the different attributes. It implements several additional methods that transform original attributes in more manageable attributes. eg. from the FLAG attribute the actual strand is extracted etc.
# Check if the record corresponds to a match my $mapped = $sam_record->is_mapped; # Check if the record corresponds to a non match my $unmapped = $sam_record->is_unmapped; # Parse the FLAG attribute and return 1 or -1 for the strand my $strand = $sam_record->strand;
To install GenOO, copy and paste the appropriate command in to your terminal.
cpanm
cpanm GenOO
CPAN shell
perl -MCPAN -e shell install GenOO
For more information on module installation, please visit the detailed CPAN module installation guide.