This file describes the making of the IBDgraph C-library, and how to run the resulting executable on test examples. A copy of this text file is included in the IBDgraph directory under the name INSTALL_C.txt. ********************************************************** To build the library, run make libdgl This will create an executable, dglgraphs. To remove the *.o files from the src subdirectorory, run make clean It is recommended you run make clean before and after making your library on a new machine. To remove the executable as well as the *.o files run make ultraclean ******************************************************** Tests may be run using the executable dglgraphs, however, number of graphs and number of edges is now required input. Hence, the generic command to run the program is as follows: ./dglgraphs NOTE: Spaces are used between all input parameters, as opposed to the previous python script where this was not required. For a list of options and input format, run either ./dglgraphs -h ./dglgraphs --help Two example test files are in subdirectory tests/datafiles: test_dgl_1.dglf1 and test_dgl_2.dglf1 (The third file is the combination of these two) Note that both files contain 100 graphs, but differing numbers of edges: test_dgl_1.dglf1 has 6 edges test_dgl_2.dglf2 has 14 edges (There is also a larger example; tests/datafiles/subpedb_snps201_reduce.dgl) This one has 8 observed individuals, and 1000 graphs, over 201 markers.) To run the example, obtaining the graphs equivalent across all markers: ./dglgraphs tests/datafiles/test_dgl_1.dglf1 100 6 To run the example, obtaining the graphs equivalent at a specific marker: e.g. marker 3 ./dglgraphs tests/datafiles/test_dgl_1.dglf1 100 6 -m 3 To run the example, obtaining the graphs equivalent over a marker range: e.g. between markers 3 and 5, ./dglgraphs tests/datafiles/test_dgl_1.dglf1 100 6 -r 3 5 IMPLEMENTED, but still needs work to fix. To run the example, obtaining for a particular graph and specified marker, how far in each direction the graph remains equivalent, e.g. graph number 65 around marker 5 run ./dglgraphs tests/datafiles/test_dgl_1.dglf1 100 6 -s 65 5 which will return "The hash at marker 5 is valid for the marker range 2 to +Inf" WORKS, but still needs work on output format. To run the example, and obtaining all the marker intervals where a particular graph is equivalent, e.g. graph number 65, run ./dglgraphs tests/datafiles/test_dgl_1.dglf1 100 6 -a 65 ********************************************************** Have fun!! Elizabeth Thompson Updated: August 10, 2010 **********************************************************