Merge pull request #1 from cancerit/dev

Worked through changes with @AndyMenzies, looks good.
Merge pull request #3 from cancerit/dev

Prep v.1.1.0
Merge pull request #4 from cancerit/dev

Pull C alleleCounter code and improvements to perl efficiency
Merge pull request #5 from cancerit/dev

Fixed up the setup.sh script to install the C version of the code
Merge pull request #6 from cancerit/dev

fixed issue with availability of samtools header files for alleleCounter...
Merge pull request #7 from cancerit/dev

Updated to last stable samtools before htslib
Merge pull request #8 from cancerit/master

Sync with master