Add utility method to get list of available read-groups
Replace SM RG tag to match provided sample name
Make thread join interval modifiable
added check to ensure readgroup ID uniqueness within all BAMs processed together, usually all BAMs belong to the same donor. also changed regex for the PU field which allows run name to have underscores in them
Merge pull request #30 from junjun-zhang/dev

added check to ensure readgroup ID uniqueness within all BAMs processed ...
Upgrade biobambam version and minor enhancements
Merge pull request #31 from ICGC-TCGA-PanCancer/dev

Dev - merge 1.0.1 to master for release
Ensure exporter::progressive is indicated as dependency
Prevent problems when reinstalling if pathed perl doesn't match /usr/bin/perl version
as we can't tell if *.gz is razf or gzip go for the safest option and decompress ready for bamsorts nm/md correction
add relevant support for md/nm recal
Add ability to allow stdout/err redirect to file when Threads processing to be disabled
Update biobambam and bwa dependencies
Prevent race condition on decompression of ref
Release 1.0.2, updated docs, version and upgrade path
Merge pull request #32 from ICGC-TCGA-PanCancer/dev

Dev - merge 1.0.2 for release
Correct issue in upgrade path for bwa

Need to improve this in future releases
Correct hash ref keys request

Fixes #33, identified at compile time by perl 5.18, previously only on access. Not used by submission code.
Sorted and added BTCA-SG
moved testData into t/data to clean up the structure