Merge pull request #1 from js21/master

First commit with most of the codebase in place
Merge pull request #2 from js21/master

All dependencies in place and all tests passed
Merge pull request #3 from js21/master

Only necessary modules in repo.
Merge pull request #4 from js21/master

Tests all pass with the new directoryt structure
Merge pull request #5 from js21/master

Can build with dzil build. All tests pass dzil test
Merge pull request #6 from js21/master

Redefined the module call Bio::RNASeq::StandardProtocol::Read on the Ali...
Merge pull request #10 from js21/master

Total Mapped Reads method fucntionality added
Merge pull request #11 from js21/master

Option handling properly implemented. Also new method for creating total_mapped_reads started
Merge pull request #12 from js21/master

Added new RPKM calculation method based on total reads mapped to gene mo...
Merge pull request #13 from js21/master

Tests for the Expression.pm object are fully implemented. Size reduction...
Merge pull request #14 from js21/master

All tests for all protocols and total mapped read methods implemented.
Merge pull request #15 from js21/master

Complete restructuring of the code
Merge pull request #16 from js21/master

Another minor formatting issue on README
Merge pull request #17 from js21/master

Minor corrections to requires section of README.md
Merge pull request #18 from js21/master

Added the Sam.pm module as it was actually required by BAMstats.pm
Merge pull request #19 from js21/master

Reimplementation of the total number of reads that mapped, plus deletion of several modules
Merge pull request #20 from js21/master

Last cleanup of not used modules
Merge pull request #21 from js21/master

Cleaned up the application
Merge pull request #22 from js21/master

GFF3 concatenator utility added
Merge pull request #23 from js21/master

Tests needed for lack of cmd args