Merge pull request #1 from wtsi-npg/devel

Release 1.11
Merge branch 'devel' of git://github.com/KateTaylor/illumina2bam into devel
New test and proposed fix for EXCLUDE_UNALIGNED = true and default
S=Y,MT
Experiment with test merge
Delete test files on exit
Merge tests that share test data
Timestamped directory experiment
Remove test output from git repository
AlignmentFilterTest to use three subdirectories in testdata for output to avoid threading clases on output files
Merge remote changes from origin
Merge first two tests as second test uses output of first.
Use named directories for AlignmentFilterTest
as per AlignmentFilterMetricTest; merge tests for MD5 checks with the
test producing the file.
Merge all tests and object creation/teardown for successful case
remove unnecessary test directories
Leave the @Before/AfterClass notations for FilterFileReader
PosFileReader and SCLFileReader to see if these get threaded as well,
merge into test for CLocsFileReader
Merge OK tests but not @Before/AfterClass tags
Merge related tests, move Lane declaration from global
Release 1.12: prevent tests running out of order
Remove test output from repository; add asserts
Streamline logic, independent output paths for test data