--outSAMunmapped Within some reads being lost

[alexander-e-f-smith]

          Hiya. Realized I'd not responded to this and just revisiting this for a pipeline update.  I do use ```--outSAMunmapped Within``` but still get this behaviour: some reads being lost (ie one of a pair lost - ie no longer seen in output bam based on read name while being found as expected in input fastq). Plenty of unaligned/improper pairs (where only one of mate of pair is aligned) do make it into bam as expected using  ```--outSAMunmapped Within``` ,  but it seems some don't and are subsequently found as single reads in output bam file.

Originally posted by @alexander-e-f-smith in #1842 (comment)