Merge pull request #4 from wtsi-npg/devel

Merge pull request #3 from wtsi-npg/master
Merge pull request #2 from wtsi-npg/devel

Devel
Merge pull request #5 from dkj/devel

change MiSeq samplesheet writing location to sf49
Merge pull request #6 from wtsi-npg/devel

Devel
Merge pull request #7 from wtsi-npg/master

Pull 73.3 tag
webinstall tagget for build, web instructions and apache config file updated, build is uncomfortable with the version of lib/npg/view.pm as "unknown",
Merge pull request #8 from mgcam/devel

Merge pull request #2 from wtsi-npg/devel
merged changes from wtsi-devel, tag 73.3
test that resets modification time of test files is directed away from source distribution; top-level .gitignore file to stop git reacting to back-up files and files generated in a normal build
RT#313168: Re: incorrect action on "Not suitable for alignment" option - fixed
reference finder to return no reference if the sample is not suitable for alignment RT#313168; reference finder refactored to ensure that abs_path is called on existing directories; tests improvements
Was getting cryptic "Undefined subroutine &Carp::shortmess_heavy called at /software/perl-5.8.8/lib/5.8.8/Carp.pm line 260" errors in webserver. Swapping "use lib" and "use warnings" resolves this problem, Carp comes from our owm cpan modules. Why Native Carp stopped cooperation is unclear.
Merge pull request #9 from mgcam/devel

Devel

Built tests, discussed code changes with mgcam.
Merge pull request #10 from wtsi-npg/devel

pull from wtsi devel to wtsi master for release 73.4
Merge pull request #11 from wtsi-npg/master

pull tagged master 73.4 to devel
Merge pull request #3 from wtsi-npg/devel

pull changes from wtsi devel to my devel
mysql client does not read configuration in default places to avoid reading wrong configuration; use password for the root user on a local test database; README - extended description of npg_tracking namespace
Merge pull request #12 from mgcam/devel

Devel
WTSI MiSeqs configured to produce HTML based RTA reports - so re-enable this link for them