Added argument 'flavor' to BwaAlignment for specifying algorithm.  Currently only 'backtransform' is supported, but we should also support 'mem' from 2013.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3605 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Version: 0.4.39 [2014-04-13]
o Added buildDictionary() for FastaReferenceFile.  Required by GATK.
o ROBUSTNESS: Now gatk() throws GATK errors as R errors.
o ROBUSTNESS: Added package system test for gatk().


git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3606 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
o Now setupExampleData() includes GATKResourceBundle data, iff GATK and its resource bundle is available.


git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3607 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3608 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Bah, hopefully the low-level GATK test will work now.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3609 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Now outputting <name>.dict from <name>.fasta - not <name>.fasta.dict.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3610 edb9625f-4e0d-4859-8d74-9fd3b1da38cb