diff --git a/readme.md b/readme.md index cc6cb03..88a4240 100644 --- a/readme.md +++ b/readme.md @@ -20,8 +20,8 @@ The problem of pairing TCRA/TCRB sequences thus reduces to the "assignment probl matching on a bipartite graph--the subset of vertex-disjoint edges whose weights sum to the maximum possible value. This is a well-studied combinatorial optimization problem, with many known solutions. -The most efficient algorithm known to the author for maximum weight matching of a bipartite graph with strictly integral weights -is from Duan and Su (2012). For a graph with m edges, n vertices per side, and maximum integer edge weight N, +The most efficient algorithm known to the author for maximum weight matching of a bipartite graph with strictly integral +weights is from Duan and Su (2012). For a graph with m edges, n vertices per side, and maximum integer edge weight N, their algorithm runs in **O(m sqrt(n) log(N))** time. As the graph representation of a pairSEQ experiment is bipartite with integer weights, this algorithm is ideal for BiGpairSEQ. @@ -203,8 +203,9 @@ Options for creating a Graph/Data file: These files do not have a human-readable structure, and are not portable to other programs. -(For portability to other software, turn on GraphML output in the Options menu. This will produce a .graphml file -for the weighted graph, with vertex attributes sequence, type, and occupancy data.) +(For portability to other software, turn on GraphML output in the Options menu in interactive mode, or use the -graphml +command line argument. This will produce a .graphml file for the weighted graph, with +vertex attributes for sequence, type, and occupancy data.) ---