InstData Import flagstat and metrics modifications.

There is an alternative (probably better) way to infer paired_end status at line 689 of Genome::InstrumentData::AlignmentResult.  
my $stats = Genome::Model::Tools::Sam::Flagstat->parse_file_into_hashref($output_file);
my $percent_paired = $stats->{reads_paired_in_sequencing} / $stats->{total_reads};
my $is_paired_end = 1 if $percent_paired >= 0.9;

Boundary 0.9 was arbitrarily chosen though.