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Checkout the code from

svn://svn.code.sf.net/p/ms-and/code

Linux:

1. compile the code:

   g++ -o msand main.cpp

2. run the sample:

   ./msand ../samples/results.txt ../samples/chr18_1st.gff ../samples/chr18_3rd.gff ../samples/chr18_wb.gff

3. View the results using (Nimblegen or) an editor in the file:

   ../samples/results.txt

Windows (from within Visual Studio):

1. Load and build embryo.sln

2. Set the program arguments by right clicking on the project embryo --> Properties --> Debugging --> Command Arguments:

   ../../samples/results.txt ../../samples/chr18_1st.gff ../../samples/chr18_3rd.gff ../../samples/chr18_wb.gff

3. Run the program (F5)

4. View the results using (Nimblegen or) an editor in the file:

   ../../samples/results.txt