InstData Import flagstat and metrics modifications.

I think is_paired_end maybe a misnomer, and could mean different things at different times. For import purposes, is paired end means there is a read 1 & 2 for each template. If reads are missing, problems can occur during alignment. This will eventually be moved into a validator, which will also check quality scores.

The formula above just sees that readsd are marked as paired constitue at least 90% of the reads. This could cause problems for aligners. Here are those stats and what they mean:

total_reads
total lines in sam excluding headers
samtools view $bam | wc -l

reads_paired_in_sequencing
reads that have the is_paired flag set
samtools view -f 0x0001 $bam | wc -l