combine trim_adjacency_matrix with construct_graph

[dmarx]

Ultimately, we just iterate through the condensed adjacency matrix anyway. Instead of creating a (potentially very expensive) copy, modify the conditional test in construct_graph to test if an entry is below the 'r' threshold instead of testing if the entry is non-zero.

All we need to do is add r and rq as parameters to construct_graph and move the chunk that calculates r from rq to the top of construct_graph.

The result should be moderately faster (the real bottleneck in the code is the pdist call) and much more memory efficient.