Merge pull request #42 from iainrb/devel

Merge changes from iainrb/devel for version 1.07
Merge pull request #43 from wtsi-npg/devel

Merge in changes from wtsi-npg/devel for version 1.07
Merge pull request #44 from iainrb/devel

Merge changes from iainrb/devel for version 1.08
Merge pull request #45 from wtsi-npg/devel

Merge in changes from wtsi-npg/devel for version 1.08
Merge pull request #46 from iainrb/devel

Allow cycle range by read to be specified on command line
Merge pull request #47 from iainrb/devel

Update version to 1.09
Merge pull request #48 from wtsi-npg/devel

Merge in changes from wtsi-npg/devel for version 1.09
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
Bump hardcoded version strings and update Changes
Merge remote branch 'upstream/devel' into npgupstreammaster

Conflicts:
	nbproject/project.properties
Merge pull request #52 from wtsi-npg/master

Merge 1.10 back into devel