Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop

Conflicts:
	Makefile
Merge branch 'develop' of https://github.com/samtools/samtools into develop

Conflicts:
	Makefile
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Merge branch 'develop' of https://github.com/samtools/samtools into develop
Added a test for specifying the reference via samtools -T.  This
appeared to work in our previous tests, but did not due to the code
sneakily reverting to the @SQ UR: field instead.
Merge branch 'develop' of https://github.com/samtools/samtools into develop