# DPAligner

Aligners with a dynamic programming foundation. Essentially Smith-Waterman variants. Issues considered include modularisation, optimisation, graph specialisation.

## Dependencies

Catch - A header-only unit testing framework.  Included as a submodule.

## Build

You will need cmake on the command line. 

1. Get the source: `git clone --recurse [email protected]:hardlianotion/dpaligner.git`
2. Create a build directory: `mkdir <root>/build`
3. Generate project files (makefiles in this case): `cd build; cmake -G "Unix Makefiles"`
4. Create library and test executable from the build directory: `make`
5. run tests: `<root>/build/test/testRun`

And you should see at least one passing test...

Warning:
Because the library sources are globbed from cpp files under <root>/source, cmake cannot currently detect changes in the source files list that make up the library.  So for now, cmake -G <generator> <path-to-root-from-build> should be run after every addition to or subtraction from the source file list.