Output reads not paired with a mixture of single end and paired end reads when using smart-pairing

[nh13]

If there is an odd number of single end reads in the first chunk read in by bwa, then potentially paired end reads in subsequent blocks may not have their pair flag set.

BWA reads in a fixed # of individual records, THEN checks for pairing, so if a paired end read spans the chunk boundary, they wont be paired.