Add test for AlignmentMerge with single fragment read data
don't call paired-end specific routines for single-ended data
Merge remote branch 'srl-local/devel' into devel
Fix test for AlignmentMerge with single fragment read data
Fix order of arguments in AssertsEquals so that failure messages make sense.
Fix order of arguments in AssertsEquals so that failure messages make sense.
Use newer Picard (1.84 instead of 1.72) and update md5 values in tests due (presumably) to reported BAM format version change from 1.0 to 1.4
Merge pull request #49 from dkj/devel

Bugfix - AlignmentFilter should cope with single read/fragment data
Merge branch 'devel' of github.com:wtsi-npg/illumina2bam into devel
Merge pull request #50 from dkj/devel

Use newer Picard
Merge remote branch 'upstream/devel' into npgupstreammaster

Conflicts:
	nbproject/project.properties