remove warnings from new compiler
Merge remote-tracking branch 'wtsi-npg/devel' into devel
typo
updated location of samtools
Modernise autotools and fix some platform specific stuff

Modernise autoconf
Modernise automake
Properly quote to avoid AC_LANG_SOURCE error
Change version.h to work on platforms which don't have echo -n
set pipefail so errors in samse/pe cause script to fail
Merge pull request #81 from mp15/autotools

Modernise autotools and fix some platform specific stuff
Merge pull request #82 from srl147/devel

Capture aligner exits in wrapper script.
Move exit check outside function (reading calibration table).
Merge pull request #83 from wtsi-npg/devel

v10.14