initial commit
Initial commit; essentially a bunch of hacking so far
added ability to count unique kmers present in RNASeq database
Update to include NNLS solver and related code
added external directory for the logger
add a lot of code missing from the repository.
Update with new Indexer interface and pipeline interface
updates to pipeline scritpt & iterative optimizer
update repo for initial move to Lane cluster
Updated sailfish to remove unused methods.  Added index as subcommand of sailfish rather than its own program.
commented out unused headers
Commented out unnecessary external dependencies in CMake files
Moved implementation of Sailfish index over from sorted array to
perfect hash.  For some strange reason, git marked all of the files
in the working directory as deleted before this commit.  I added
them all back in --- hopefully, this won't break anything!
after stupidly deleting all of the plotting scripts from my local directory when wanting to check out a fresh version of the repo, I had to spend the night rewriting them.  I believe the current scripts reproduce the functionality (and results) of the original scripts . . . that sucked
re-incorporating poisson model estimation ... may not compile yet
massive commit; will try to begin the migration to the lane cluster
Major update to cmake build.  All major dependencies (aside from Boost) are automatically fetched and built as part of the Sailfish build process.
Build can now fetch and compile all non-boost dependencies as well as build source and binary packages
Updated command line interface.  There is now an \'exposed\' simple interface for the end-user, while the original interface remains \'hidden\' for power-users.
Major overhaul to command line interface and index file layout.  Added LICENSE information to the top-level directory and added license header to all files.  Sailfish now automatically checks version information online when it's started