Initial directory structure.
Initial commit
* Added ScaffoldExtractor
* Changed DPGraph to matrix representation
* Updated a couple of solvers? why and what?
* Updated contig splitting code to record 5' contig coordinates
* Updated Helpers
* Fixed coordinate calculation
Major update
1) Created common directory
2) Changed a lot (SVN client wasn't working)
3) Added k-mer statistics generator
4) Added GraphViz support
5) Added EMSolver
6) Fixed DPSolver
- Fixed typos in Configuration help
- Fixed typos
- Cleaned up
- Fixed BnB to use constants from ExtendedFixedMIQPSolver
- Fixed compilation time bug related to definition of desired slacks
- Fixed a SIGSEGV in BnB and a bug in FixedMIQPSolver formulate
- Stupid return 0; bug in GetOrderSlack
cost 12 hours to find (only showed up in BnB and it wasn't evident even)
- Cleaned up BranchAndBound
- Cleaned up ExtendedFixedMIQPSolver
- Cleaned up
- Fixed includes
- Added scaffold output to main()
- Fixed opportunistic search bug (sometimes it's enabled by default, so we have to enforce the setting we want).
- Last commit did not fix the problem => a new one ;)
- Added no-overlap-deviation support
- Added BWA exact alignment support