o SPEEDUP: Now readSeqLengths() for FastaReferenceFile memoizes results.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3618 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
o Now getDefaultFullName() for FastqDataFile drops PE suffixes.
o Added field 'paired' to FastqDataFile.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3619 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Tagging tests as either SE or PE.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3620 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Updated Rd's.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3621 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3622 edb9625f-4e0d-4859-8d74-9fd3b1da38cb