Merge pull request #42 from dkj/devel

Fix dodgy merge resolution
Merge pull request #43 from dkj/devel

Comment fix and vestigial code removal
moved flagstat after spatial_filter
fixed typo
Merge pull request #45 from srl147/devel

moved flagstat after spatial_filter and check for properly paired count rather than pairs aligned
Merge pull request #46 from wtsi-npg/devel

prep for release