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Update readme with -graphml flag

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efischer
2022-03-01 08:24:43 -06:00
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@@ -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. 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. 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 The most efficient algorithm known to the author for maximum weight matching of a bipartite graph with strictly integral
is from Duan and Su (2012). For a graph with m edges, n vertices per side, and maximum integer edge weight N, 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 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. 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. 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 portability to other software, turn on GraphML output in the Options menu in interactive mode, or use the -graphml
for the weighted graph, with vertex attributes sequence, type, and occupancy data.) command line argument. This will produce a .graphml file for the weighted graph, with
vertex attributes for sequence, type, and occupancy data.)
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