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
ensure we use fixed location for bwa throughout script
ensure we fail early on not finding bwa
Merge pull request #47 from dkj/devel

ensure we use consistent bwa throughout script
Merge branch 'wtsi-npg/devel' into devel

Conflicts:
	bin/pb_align